Aside

Rüçhan Ekren

Contact

Technical Capabilities

R (Base)
R (Markdown)
R (Tidyverse)
Bash
Linux Terminal
Git
Slurm
Conda
Docker
Python
Jupyter
NextFlow
nf-core

Main

Rüçhan Ekren

Currently PhD student in Bioinformatics with the expected thesis manuscript submission of Auguts 2023. Mainly working on scRNAseq data curation and its robust analysis.

Education

Bioinformatics, Genomics and Systems Biology

Paul Sabatier University of Toulouse III

Toulouse, FR

Current - 2020

  • PhD Candidate
  • Thesis: The Alterations of Transcriptomic Program of Natural Killer Cells in the Tumor Microenvironment of Mutiple Myeloma

Biostatics and Bioinformatics

Acibadem University

Istanbul, TR

2020 - 2017

  • Master of Science
  • Thesis: Transcriptomics-based Investigation of Drug Resistance Mechanisms in Triple-negative Breast Cancer Cell Lines

Molecular Biology & Genetics

Izmir Institute of Technology

Izmir, TR

2016 - 2011

  • Bachelor of Science

Research Experience

Bioinformatics Analyst

GENIM - CRCT

Toulouse, FR

Current - 2020

  • Establishing robust, end-to-end scRNAseq analysis pipeline with improved QC steps involved
  • Being in charge of orchestration of 40 human scRNAseq samples and complementary 4 mouse scRNAseq samples
  • Characterization of corresponding cell types with supervised and unsupervised approaches within cohort
  • Functional analyses such as differential expression, pathway enrichment, and trajectory inference analyses

Graduate Reearch Assistant

Sezerman Bioinformatics Lab

Istanbul, TR

2020 - 2017

  • Transcriptome Profile Analysis of Atherosclerosis Rabbit Model from pooled CEL-Seq2 Data
  • Investigation of miRNA Activity-related Mechanisms of Drug Resistance on Breast Cancer Patients from RNA-Seq data
  • Transcriptomics Analysis of Insulin-resistant Rat Model from Microarray data

Research Assistant

JLab Bioinformatics

Izmir, TR

2016 - 2015

  • Processing publicly available NGS data from “1000 Genome project” to find alternative explanations of cancer causes
  • Sequential mapping of genomic reads to human reference genome, bacteria genome pool and then viral genome pool

Undergraduate Researcher

Controlled in vitro Microenvironments Lab

Izmir, TR

2015 - 2012

  • Optimization of PDA liposome embedded assay with breast cancer cell laden
  • Fabrication of the polydiacetylene (PDA) / polyvinylalcohol (PVA) electrospun mats for cell culture applications
  • Lab-on-a-chip biosensor development for rapid bacteria detection

Visiting Researcher

Internal Medicine Lab - Universitätsklinikum

Tübingen, GR

2014

  • Disruptive Effect of Dietary Ethanol Stimulation on Cholangiocarcinoma cells




Teaching Experience

Omics

Acibadem University

Istanbul, TR

2020 - 2018

  • Teaching Assistant
  • Detailed theoretical explanation of RNA-Seq, data analysis pipeline and hands-on experience with supervised term projects
  • Undergraduate class to medicine students

RNA-Seq Analysis

Acibadem University

Istanbul, TR

2018

  • Within the framework of EpiSyStem (Epigenetics and System Biology of Stem cells and Reprogramming) of H2020:Marie Curie Innovative Training Networks
  • Handled the organization and being teaching assistant of the workshop
  • With the focus of how to leverage RNA-seq data, its analysis and practical applications

Published articles

CD137(4-1BB) Signaling Drives a TcR-Independent Exhaustion Program in CD8 T Cells

Immunity -in press-

N/A

2022

Response Assessment With Molecular Characterization of Circulating Tumor Cells and Plasma MicroRNA Profiling in Patients With Locally Advanced Breast Cancer During Neoadjuvant Chemotherapy

Clinical Breast Cancer

N/A

2020

Transcriptomics-based Investigation of Drug Resistance Mechanisms in Triple-negative Breast Cancer Cell Lines

Master Thesis

N/A

2020

Ameliorative potential of Lavandula stoechas in metabolic syndrome via multitarget interactions

Journal of Ethnopharmacology

N/A

2018




Selected Conferences and Seminars

CARe Bionformatics Workshop

Amphitheatre Oncopole

Toulouse, FR

2022

  • Selected to give scientific talk about my current project by scientific commitee.

NextflowSummit 2022

Virtual Event

Barcelona, SP

2022

Network Science in Biology and Medicine (NetBioMed)

Virtual Event

Washington DC, USA

2021

  • Presented scientific poster about my current project

Les Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM)

Institut Pasteur, Virtual Event

Paris, FR

2021

  • Presented scientific poster about my current project

Computational Systems Biology of Cancer: Multi-omics and Machine Learning Approaches (SysBioCancer)

Institut Curie, Virtual Event

Paris, FR

2021

  • Selected for doing oral presentation about my current project by scientific commitee

Combination in cancer immunotherapy resistance, from molecular aspects to clinical issues (CICOR)

Amphitheatre Oncopole

Toulouse, FR

2021

  • Selected for giving a scientific talk about my current project by scientific commitee

Single-cell Genomics Day

Virtual Event

New York, USA

2021

Computational Genomics. A Hands-on Course on Machine Learning for Genomics

Virtual Bootcamp, Max Delbrück Center

Berlin, GR

2021

Extra-curriculum Activities

I also enjoy reading fictional literature, climbing, playing story-rich role-playing video games, and doing woodcarving in my free time.

International Society for Computational Biology (ISCB)

N/A

N/A

Current - 2023

  • Student member

COMmitee ETudiant (COMET)

N/A

N/A

Current - 2022

  • Responsible for the organization of journal clubs, workshops and other events for the students of CRCT

Société Française de Bioinformatique (SFBI)

N/A

N/A

Current - 2021

  • Student member

European Association for Cancer Research (EACR)

N/A

N/A

Current - 2021

  • Student member

CARe Training Council

N/A

N/A

Current - 2021

  • In charge of preparing the prospective members of the Cancer, Aging, and Rejuvanation (CARe) Graduate School

Hope Foundation for Children with Cancer (KACUV)

N/A

N/A

Current - 2021

  • Volunteer and donor of the foundation

Tutorship

N/A

N/A

2020 - 2018

  • Volunteered tutorship for middle school kids on science and math courses

Disclaimer

This CV is made with the R packages pagedown and datadrivencv.

The public repository of this CV is hosted in here

Last updated on 2023-05-19.